Mind the Gap: Molecular Architecture of the Axon Initial Segment - From Fold Prediction to a Mechanistic Model of Function?

Na+/K+-ATPase: ion pump, signal transducer, or cytoprotective protein, and novel biological functions

Na+/K+-ATPase is a transmembrane protein that has important roles in the maintenance of electrochemical gradients across cell membranes by transporting three Na+ out of and two K+ into cells. Additionally, Na+/K+-ATPase participates in Ca2+-signaling transduction and neurotransmitter release by coordinating the ion concentration gradient across the cell membrane. Na+/K+-ATPase works synergistically with multiple ion channels in the cell membrane to form a dynamic network of ion homeostatic regulation and affects cellular communication by regulating chemical signals and the ion balance among different types of cells. Therefore, it is not surprising that Na+/K+-ATPase dysfunction has emerged as a risk factor for a variety of neurological diseases. However, published studies have so far only elucidated the important roles of Na+/K+-ATPase dysfunction in disease development, and we are lacking detailed mechanisms to clarify how Na+/K+-ATPase affects cell function. Our recent studies revealed that membrane loss of Na+/K+-ATPase is a key mechanism in many neurological disorders, particularly stroke and Parkinson's disease. Stabilization of plasma membrane Na+/K+-ATPase with an antibody is a novel strategy to treat these diseases. For this reason, Na+/K+-ATPase acts not only as a simple ion pump but also as a sensor/regulator or cytoprotective protein, participating in signal transduction such as neuronal autophagy and apoptosis, and glial cell migration. Thus, the present review attempts to summarize the novel biological functions of Na+/K+-ATPase and Na+/K+-ATPase-related pathogenesis. The potential for novel strategies to treat Na+/K+-ATPase-related brain diseases will also be discussed.

Assessing Fairness of AlphaFold2 Prediction of Protein 3D Structures

AlphaFold2 is reshaping biomedical research by enabling the prediction of a protein's 3D structure solely based on its amino acid sequence. This breakthrough reduces reliance on labor-intensive experimental methods traditionally used to obtain protein structures, thereby accelerating the pace of scientific discovery. Despite the bright future, it remains unclear whether AlphaFold2 can uniformly predict the wide spectrum of proteins equally well. Systematic investigation into the fairness and unbiased nature of its predictions is still an area yet to be thoroughly explored. In this paper, we conducted an in-depth analysis of AlphaFold2's fairness using data comprised of five million reported protein structures from its open-access repository. Specifically, we assessed the variability in the distribution of PLDDT scores, considering factors such as amino acid type, secondary structure, and sequence length. Our findings reveal a systematic discrepancy in AlphaFold2's predictive reliability, varying across different types of amino acids and secondary structures. Furthermore, we observed that the size of the protein exerts a notable impact on the credibility of the 3D structural prediction. AlphaFold2 demonstrates enhanced prediction power for proteins of medium size compared to those that are either smaller or larger. These systematic biases could potentially stem from inherent biases present in its training data and model architecture. These factors need to be taken into account when expanding the applicability of AlphaFold2.

Neurofilament accumulations in amyotrophic lateral sclerosis patients' motor neurons impair axonal initial segment integrity

Amyotrophic lateral sclerosis (ALS) is the most common motor neuron (MN) disease in adults with no curative treatment. Neurofilament (NF) level in patient' fluids have recently emerged as the prime biomarker of ALS disease progression, while NF accumulation in MNs of patients is the oldest and one of the best pathological hallmarks. However, the way NF accumulations could lead to MN degeneration remains unknown. To assess NF accumulations and study the impact on MNs, we compared MNs derived from induced pluripotent stem cells (iPSC) of patients carrying mutations in C9orf72, SOD1 and TARDBP genes, the three main ALS genetic causes. We show that in all mutant MNs, light NF (NF-L) chains rapidly accumulate in MN soma, while the phosphorylated heavy/medium NF (pNF-M/H) chains pile up in axonal proximal regions of only C9orf72 and SOD1 MNs. Excitability abnormalities were also only observed in these latter MNs. We demonstrate that the integrity of the MN axonal initial segment (AIS), the region of action potential initiation and responsible for maintaining axonal integrity, is impaired in the presence of pNF-M/H accumulations in C9orf72 and SOD1 MNs. We establish a strong correlation between these pNF-M/H accumulations, an AIS distal shift, increased axonal calibers and modified repartition of sodium channels. The results expand our understanding of how NF accumulation could dysregulate components of the axonal cytoskeleton and disrupt MN homeostasis. With recent cumulative evidence that AIS alterations are implicated in different brain diseases, preserving AIS integrity could have important therapeutic implications for ALS.

Crystal structure of Ankyrin-G in complex with a fragment of Neurofascin reveals binding mechanisms required for integrity of the axon initial segment

The axon initial segment (AIS) has characteristically dense clustering of voltage-gated sodium channels (Nav), cell adhesion molecule Neurofascin 186 (Nfasc), and neuronal scaffold protein Ankyrin-G (AnkG) in neurons, which facilitates generation of an action potential and maintenance of axonal polarity. However, the mechanisms underlying AIS assembly, maintenance, and plasticity remain poorly understood. Here, we report the high-resolution crystal structure of the AnkG ankyrin repeat (ANK repeat) domain in complex with its binding site in the Nfasc cytoplasmic tail that shows, in conjunction with binding affinity assays with serial truncation variants, the molecular basis of AnkG–Nfasc binding. We confirm AnkG interacts with the FIGQY motif in Nfasc, and we identify another region required for their high affinity binding. Our structural analysis revealed that ANK repeats form 4 hydrophobic or hydrophilic layers in the AnkG inner groove that coordinate interactions with essential Nfasc residues, including F1202, E1204, and Y1212. Moreover, we show disruption of the AnkG–Nfasc complex abolishes Nfasc enrichment at the AIS in cultured mouse hippocampal neurons. Finally, our structural and biochemical analysis indicated that L1 syndrome-associated mutations in L1CAM, a member of the L1 immunoglobulin family proteins including Nfasc, L1CAM, NrCAM, and CHL1, compromise binding with ankyrins. Taken together, these results define the mechanisms underlying AnkG–Nfasc complex formation and show that AnkG-dependent clustering of Nfasc is required for AIS integrity.

Neuronal metabolism in learning and memory: The anticipatory activity perspective

Current research on the molecular mechanisms of learning and memory is based on the "stimulus-response" paradigm, in which the neural circuits connecting environmental events with behavioral responses are strengthened. By contrast, cognitive and systems neuroscience emphasize the intrinsic activity of the brain that integrates information, establishes anticipatory actions, executes adaptive actions, and assesses the outcome via regulatory feedback mechanisms. We believe that the difference in the perspectives of systems and molecular studies is a major roadblock to further progress toward understanding the mechanisms of learning and memory. Here, we briefly overview the current studies in molecular mechanisms of learning and memory and propose that studying the predictive properties of neuronal metabolism will significantly advance our knowledge of how intrinsic, predictive activity of neurons shapes a new learning event. We further suggest that predictive metabolic changes in the brain may also take place in non-neuronal cells, including those of peripheral tissues. Finally, we present a path forward toward more in-depth studies of the role of cell metabolism in learning and memory.

Axon-Targeting Motifs: Mechanisms and Applications of Enhancing Axonal Localisation of Transmembrane Proteins

Neuronal polarity established in developing neurons ensures proper function in the mature nervous system. As functionally distinct cellular compartments, axons and dendrites often require different subsets of proteins to maintain synaptic transmission and overall order. Although neurons in the mature CNS do not regenerate throughout life, their interactions with their extracellular environment are dynamic. The axon remains an overall protected area of the neuron where only certain proteins have access throughout the lifespan of the cell. This is in comparison to the somatodendritic compartment, where although it too has a specialised subset of proteins required for its maintenance, many proteins destined for the axonal compartment must first be trafficked through the former. Recent research has shown that axonal proteins contain specific axon-targeting motifs that permit access to the axonal compartment as well as downstream targeting to the axonal membrane. These motifs target proteins to the axonal compartment by a variety of mechanisms including: promoting segregation into axon-targeted secretory vesicles, increasing interaction with axonal kinesins and enhancing somatodendritic endocytosis. In this review, we will discuss axon-targeting motifs within the context of established neuron trafficking mechanisms. We will also include examples of how these motifs have been applied to target proteins to the axonal compartment to improve both tools for the study of axon biology, and for use as potential therapeutics for axonopathies.